The pair were both shot in the backs of their heads at close range after they left a mosque in the Queens area of the city.
Police identified the cleric as Maulama Akonjee, and his aide as 64-year-old Tharam Uddin.
Both men were wearing religious garb at the time of the shooting, but the motive was not known, said Tiffany Phillips, a spokeswoman for the New York City Police Department said, adding that there was no evidence that the pair were targeted because of their faith.
However, Muslim leaders have implied that the attack was politically motivated and blamed leaders for projecting Muslims as "the enemy".
Imam Johari Abdul-Malik, said: "For those in leadership like Mr. Trump and Mr. Giuliani and other members of institutions that project Islam and Muslims as the enemy this is the end result of their wickedness."
Afaf Nasher, Executive Director of the Council of American Islamic Relations (CAIR) in New York called for people to speak out against Islamophobia. She said: ""Imagine your father gunned down for no reason, then let that feeling, that motivate you, to come out of your silence and I especially say this to those with influence within the community and beyond."
No one has been arrested in connection with the shooting which took place as the pair left the Al-Furqan Jame Masjid Mosque at around 1.50pm local time, but witnesses reported seeing a lone armed assailant fleeing the scene.
Mr Akonjee, 55, was described as a peaceful man and a central part of Ozone Park's Muslim community.
"He would not hurt a fly," Mr Akonjee's nephew, Rahi Majid, told local media. "You would watch him come down the street and watch the peace he brings."
Shahin Chowdhury, a worshipper at the mosque, said members of the community had felt animosity lately, with people cursing while passing the mosque. He said he had advised fellow community members to be careful walking around, especially when in traditional clothing.
He called Mr Akonjee a "wonderful person" with a voice that made his Koran readings especially compelling. (itv.com)